Selection bias in meta-analyses of gene-disease associations

The Big Picture of Neurodegeneration: A Meta Study to Extract the Essential Evidence on Neurodegenerative Diseases in a Network-Based Approach

The common features of all neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, Amyotrophic Lateral Sclerosis (ALS), and Huntington's disease, are the accumulation of aggregated and misfolded proteins and the progressive loss of neurons, leading to cognitive decline and locomotive dysfunction. Still, they differ in their ultimate manifestation, the affected brain region, and the kind of proteinopathy. In the last decades, a vast number of processes have been described as associated with neurodegenerative diseases, making it increasingly harder to keep an overview of the big picture forming from all those data. In this meta-study, we analyzed genomic, transcriptomic, proteomic, and epigenomic data of the aforementioned diseases using the data of 234 studies in a network-based approach to study significant general coherences but also specific processes in individual diseases or omics levels. In the analysis part, we focus on only some of the emerging findings, but trust that the meta-study provided here will be a valuable resource for various other researchers focusing on specific processes or genes contributing to the development of neurodegeneration.

Lamivudine vs placebo or no treatment in preventing the transmission of hepatitis B virus during pregnancy: a systematic review and meta-analysis

BACKGROUND

Hepatitis B virus (HBV) infection is a severe health problem, especially in developing countries. Almost 45% of the population lives in highly endemic areas, where the most common form of transmission is mother to child transmission (MTCT). Administration of antiviral therapy has been established. Nevertheless, its efficacy still remains controversial.

METHODS

We conducted the current study to fully evaluate the effectiveness of lamivudine in preventing the MTCT of HBV based on randomized controlled trials (RCTs). Four English electronic databases and four Chinese electronic databases were searched from the inception of each database to 26 September 2017. Studies were included if they (1) were human RCT studies, (2) indicated exposure to lamivudine, (3) explicitly indicated control to placebo or no treatment, (4) indicated the participants were pregnant women infected with HBVand (5) compared the outcome of interest as the MTCT. Extracted data were tabulated and analyzed using Review Manager.

RESULTS

Eleven RCTs were included and analyzed. Compared with controls (placebo or no treatment), lamivudine significantly reduced the probability of MTCT, as indicated by newborn HBsAg seropositivity (RR=0.44, 95% CI 0.26 to 0.74, I2=41%), HBeAg seropositivity (RR=0.66, 95% CI 0.36 to 1.19, I2=0%) and HBV DNA seropositivity (RR=0.29, 95% CI 0.18 to 0.4`6, I2=0%) within 24 h after birth. Similar results were noted pertaining to infant HBsAg seropositivity and HBV DNA seropositivity within 6-7 and 12 mo.

CONCLUSIONS

Lamivudine can significantly reduce the MTCT of HBsAg and HBV DNA of neonates during the third trimester of pregnancy without severe adverse events.

Protein-protein interaction databases

Years of meticulous curation of scientific literature and increasingly reliable computational predictions have resulted in creation of vast databases of protein interaction data. Over the years, these repositories have become a basic framework in which experiments are analyzed and new directions of research are explored. Here we present an overview of the most widely used protein-protein interaction databases and the methods they employ to gather, combine, and predict interactions. We also point out the trade-off between comprehensiveness and accuracy and the main pitfall scientists have to be aware before adopting protein interaction databases in any single-gene or genome-wide analysis.

The interferon-gamma (IFN-γ) +874T allele reduces the risk of hepatitis B infection in an Asian population

Increasing evidence suggests that polymorphism of the interferon-gamma (IFN-γ) gene in the first intron at position +874 may be associated with chronic hepatitis B virus (HBV) infection and/or HBV clearance. However, the results of relevant studies have been inconsistent. To derive a more precise estimation of the association, we performed a meta-analysis. In total, 10 independent studies including 1661 chronic HBV-infected patients and 1142 controls were included in this meta-analysis. In studies following Hardy-Weinberg equilibrium (HWE), a significantly decreased risk of chronic HBV infection was associated with the IFN-γ + 874TT genotype in the overall population (TT vs AA: odds ratio (OR) = 0.714, 95% confidence interval (CI) = 0.526-0.969, P = 0.031) when compared with a spontaneously recovered population. Subgroup analysis by ethnicity revealed a similar association in Asian individuals (TT vs AA: OR = 0.706, 95% CI = 0.518-0.962, P = 0.028). Moreover, when compared with a healthy control group, the 874T allele was associated with a significant lower risk of chronic HBV infection in the overall populations (TA vs AA: OR = 0.439, 95% CI = 0.193-0.997, P = 0.049; TT + TA vs AA: OR = 0.475, 95% CI = 0.271-0.832, P = 0.009) and in Asian individuals (TA vs AA: OR = 0.862, 95% CI = 0.744-0.999, P = 0.048). In conclusion, the IFN-γ + 874TT genotype and 874T allele reduce the risk of chronic HBV infection in Asian individuals.

Relationship between IL-10 gene -1082A/G and -592C/A polymorphisms and the risk of hepatitis C infection: a meta-analysis

Increasing evidence suggests that interleukin-10 (IL-10) gene promoter polymorphisms may be associated with chronic hepatitis C virus (HCV) infection and HCV clearance. To more precisely estimate the association between these variants and the risk of HCV infection, we performed a meta-analysis of 26 studies describing the IL-10-1082A/G, -819C/T, -592C/A genotypes, including 4039 chronic HCV infection cases and 2902 controls. When compared with a healthy population, the -1082GG allele had a 43% increased risk of chronic HCV infection in combined populations (GG vs GA + AA: odds ratio (OR) = 1.433, 95% confidence interval (CI) = 1.052-1.952, P = 0.023). In subgroup analysis by ethnicity, a significant increased risk was associated with the -1082GG genotype in the Caucasian population (GG vs AA: OR = 1.390, 95% CI: 1.108-1.744, P = 0.004; GG vs GA + AA: OR = 1.621, 95% CI: 1.267-2.075, P = 0.000). However, no significant association was found in Asian, African or Chinese populations. Moreover, a higher distribution of -592A was found in the spontaneously recovered population (AA vs CC: OR = 0.585, 95% CI = 0.387-0.884, P = 0.011; AA + AC vs CC: OR = 0.738, 95% CI = 0.551-0.988, P = 0.041; AA vs AC + CC: OR = 0.788, 95% CI = 0.664-0.935, P = 0.006) than that in the chronic HCV infection population. In conclusion, the IL-10-1082GG allele may increase the risk of chronic HCV infection in Caucasian population, and people carrying the IL-10-592A allele are more likely to clear HCV spontaneously.

Three polymorphisms in the IL-10 gene and the risk of HCV infection: a meta-analysis plus a Chinese Association Study involving 1140 subjects

The influence of an immunosuppressive cytokine, interleukin-10 (IL-10), on the outcome of hepatitis C virus (HCV) infection has been increasingly reported recently. A number of polymorphisms appear to control the level of IL-10 production. Among them, −592C/A, −819C/T and −1082G/A in the IL-10 gene are three most studied single nucleotide polymorphisms. To provide a more definitive conclusion about their association with the risk of HCV infection, a meta-analysis was performed by combining and summarizing a total of 17 studies. A biological justification for the choice of genetic model was provided. The results indicated no significant association between these IL-10 polymorphisms and the susceptibility to HCV infection [–592C/A: odds ratio (OR) 0·99, 95% confidence interval (CI) 0·78–1·25; –819C/T: OR 0·90, 95% CI 0·69–1·18; –1082G/A: OR 1·34, 95% CI 0·90–2·00]. However, this analysis did not account for the possible risk modifications by other factors, such as ethnicity and virus persistence. Therefore, the effects of ethnicity and virus persistence were investigated using Bayesian meta-regression and subgroup analysis. Finally, an extended case-control association study was conducted in a Chinese population involving 1140 subjects. Both serum level and genotype data of IL-10 −1082G/A were determined. As a result, a low prevalence of G allele was observed. Significantly higher IL-10 production was observed in HCV patients, especially patients with the GG genotype.

Analysis of decisions made in meta-analyses of depression screening and the risk of confirmation bias: a case study

BACKGROUND

Depression is common in primary care and clinicians are encouraged to screen their patients. Meta-analyses have evaluated the effectiveness of screening, but two author groups consistently reached completely opposite conclusions.

METHODS

We identified five systematic reviews on depression screening conducted between 2001 and 2009, three by Gilbody and colleagues and two by the United States Preventive Task Force. The two author groups consistently reached completely opposite conclusions. We analyzed two contemporaneous systematic reviews, applying a stepwise approach to unravel their methods. Decision points were identified, and discrepancies between systematic reviews authors' justification of choices made were recorded.

RESULTS

Two systematic reviews each addressing three research questions included 26 randomized controlled trials with different combinations in each review. For the outcome depression screening resulting in treatment, both reviews undertook meta-analyses of imperfectly overlapping studies. Two in particular, pooled each by only one of the reviews, influenced the recommendations in opposite directions. Justification for inclusion or exclusion of studies was obtuse.

CONCLUSION

Systematic reviews may be less objective than assumed. Based on this analysis of two meta-analyses we hypothesise that strongly held prior beliefs (confirmation bias) may have influenced inclusion and exclusion criteria of studies, and their interpretation. Authors should be required to declare a priori any strongly held prior beliefs within their hypotheses, before embarking on systematic reviews.

Three-armed trials including placebo and no-treatment groups may be subject to publication bias: systematic review

Background

It has been argued that placebos may not have important clinical impacts in general. However, there is increasing evidence of a publication bias among trials published in journals. Therefore, we explored the potential for publication bias in randomized trials with active treatment, placebo, and no-treatment groups.

Methods

Three-armed randomized trials of acupuncture, acupoint stimulation, and transcutaneous electrical stimulation were obtained from electronic databases. Effect sizes between treatment and placebo groups were calculated for treatment effect, and effect sizes between placebo and no-treatment groups were calculated for placebo effect. All data were then analyzed for publication bias.

Results

For the treatment effect, small trials with fewer than 100 patients per arm showed more benefits than large trials with at least 100 patients per arm in acupuncture and acupoint stimulation. For the placebo effect, no differences were found between large and small trials. Further analyses showed that the treatment effect in acupuncture and acupoint stimulation may be subject to publication bias because study design and any known factors of heterogeneity were not associated with the small study effects. In the simulation, the magnitude of the placebo effect was smaller than that calculated after considering publication bias.

Conclusions

Randomized three-armed trials, which are necessary for estimating the placebo effect, may be subject to publication bias. If the magnitude of the placebo effect is assessed in an intervention, the potential for publication bias should be investigated using data related to the treatment effect.

Evidence-based practice: how to perform and use systematic reviews for clinical decision-making

One approach to clinical decision-making requires the integration of the best available research evidence with individual clinical expertise and patient values, and is known as evidence-based medicine (EBM). In clinical decision-making with the current best evidence, systematic reviews have an important role. This review article covers the basic principles of systematic reviews and meta-analyses, and their role in the process of evidence-based decision-making. The problems associated with traditional narrative reviews are discussed, as well as the way systematic reviews limit bias associated with the assembly, critical appraisal and synthesis of studies addressing specific clinical questions. The relevant steps in writing a systematic review from the formulation of an initial research question to sensitivity analyses in conjunction with the combined analysis of the pooled data are described. Important issues that need to be considered when appraising a systematic review or meta-analysis are outlined. Some of the terms that are used in the reporting of systematic reviews and meta-analyses, such as relative risk, confidence interval, Forest plot or L'Abbé plot, will be introduced and explained.

Analysis of single nucleotide polymorphisms at 13 loci within the transforming growth factor-induced factor gene shows no association with high myopia in Japanese subjects

A previous study in China first indicated that the transforming growth factor-induced factor (TGIF) is a probable candidate gene for high myopia. The purpose of our study was to investigate whether there are significant associations between high myopia and single nucleotide polymorphism (SNP) variants in the TGIF gene of Japanese subjects. Genomic DNA was collected from 330 Japanese subjects with high myopia and at a level refractive error was less than -9.25 Dsph and 330 randomized controls without high myopia. Thirteen SNPs were detected by polymerase chain reaction (PCR) and primer extension or by PCR and SNP-specific fluorogenic probes in all of the cases and controls. Thirteen SNPs were found within the TGIF genes of the cases and controls. Two of the SNPs were monomorphic and none of the 13 SNPs showed a significant result. The pairwise linkage disequilibrium (LD) mapping confirmed that these alleles have a comparatively strong LD index of >0.8 for D' and >0.4 for r(2). We found no statistical association between any of the 13 SNPs located on the TGIF gene and high myopia in Japanese subjects. Based on our study using Japanese subjects and the previous studies of TGIF gene polymorphism in Chinese and northern European subjects with myopia, there is no convincing evidence to prove a connection between nucleotide sequence variations in TGIF and high myopia.